Well, first off I would like to see all of tyhe "clone" characters be given a unique set of moves.
Also, I'd like to introduce not just color change, but costume change. I'w not talking complete character changes with new moves and stuff, jJust diffrent outfits. Suchs as, Adult Link could have OoT clothing, realistic TP clothing, and TP Civilian clothing, and NES clothing, each in their own 4 or 5 diffrent colors. You earn the new cloths, somehow. Buy with coins, play so many games with that character, whatever.
Now, characters that could warrent new, and diffrent moves, yet are versions of old characters would be fine. Such as, lets say we introduce Wind Waker Link. Now, his cartoony look could be played up. Foward smash could be the huge, loony-toon looking Never Happening Hammer from WW, whacking people unrealistically far, but requireing as power build-up (a-la Capt. Falcon) considering its large size. Down Smash could be the Iron Boots (working similar to yoshi's ground pound, yet you would have to jump and then put them on) could flatten characters and stun characters as they try to get up, looking like an accordion. Those boot would also be great to wear during high % times, yet you are virtually immobial. Paper Mario ... Well, I think you get my point here
Next I'd like the character select screen change to something that uses a tabbed interface, with each tab having the symbol for each videogame series, similar to how SSBM has character symbols. Triforce for the Zelda univers, mushroom for the Mario universe, pokeball for pokemon and maybe a tab for miscelanious characters that are the only ones of theirs series, IE, Mr. Game & Watch.
Now, to warrent the need for this interface, we'll need a good amount of new characters, I'm thinking 8 total (new+old) for each univers. Heres a quick selection of mine. (using some previous suggestions from this thread too)
(each universe represents a character select tab)
Mario Universe
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Koopa
Paper Mario
Kamek
Baby Bowser
Wario Universe
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Wario
Waluigi
8-volt (attacks with old school charm!)
Kat and Ana (duo ala-Ice Climbers)
DK Universe
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Diddy Kong
King K. Rool
Cranky Kong
Funky King (Plays DK Bongos!!!!)
F-Zero Universe
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Samurai Goroh
Pico
Black Shadow
Jody Summer
StarFox Universe
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Slippy
Peppy
Krystal
R.O.B.64
Kirby Universe
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King Dedede
Ditto
Meta Knight
Waddle Dee
Earthbound Universe
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Poo
Starman
Paula
Jeff
Pokemon Universe
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Ash
Misty
Brock
Metroid Universe
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Dark Samus
Ridley
Galatic Federation Trooper
Noxus
Zelda Universe
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Ganon
The Hero of Winds
Goron
Zora
Stalfos
Wolf Link w/ Midna
Miscelanious
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Pitt
Little Mack
Balloon Fighter
Olimar
Raimi (Geist, Posession baby!)
Doshin the Giant
Captian N